diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 6c3486d93210131097e02526667a6104b2af15a8..61e5245910a8e2066c4047db1d367abeb66a8e9c 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -1418,8 +1418,8 @@ public List<Message> alignonet( Properties params ) {
}
- /* TO VERIFY
- public Message alignonet( Properties params ) {
+ // TO VERIFY
+ public Message alignonet2( Properties params ) {
//parameters: onID, method, reflexive, symmetric
OntologyNetwork noo = null;
@@ -1435,6 +1435,7 @@ public List<Message> alignonet( Properties params ) {
} catch (AlignmentException e1) {
return new UnknownOntologyNetwork( params, newId(), serverId,id );
}
+ logger.debug(" Before Network alignments results, id: {} total ontologies: {} total alignments: {}",id, noo.getOntologies().size(),noo.getAlignments().size());
try {
((BasicOntologyNetwork) noo).match(method, reflexive, symmetric);
@@ -1448,7 +1449,32 @@ public List<Message> alignonet( Properties params ) {
}
- */
+
+ public Message trimonet( Properties params ) {
+
+ //parameters: onID, method, reflexive, symmetric
+ OntologyNetwork noo = null;
+ OntologyNetwork nooClone = null;
+ String id = params.getProperty("id");
+ String method = params.getProperty("type");
+ double threshold = Double.parseDouble(params.getProperty("threshold"));
+
+ try {
+ noo = alignmentCache.getOntologyNetwork( id );
+ //nooClone = (OntologyNetwork) ((Hashtable<URI, OntologyNetwork>) noo)).clone();
+ } catch (AlignmentException e1) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
+
+ try {
+ ((BasicOntologyNetwork) noo).trim(method, threshold);
+ } catch (AlignmentException e) {
+ return new ErrorMsg( params, newId(), serverId,"Network alignment error" );
+ }
+ return new OntologyNetworkId( params, newId(), serverId, id,
+ ((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
+ }
+
public Message listNetworkOntology( Properties params ) { //not UsED??
String result = "";
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index fddd19dde055686e8c55669019bd25998a4291c7..ee2fdec4b3578ed12285b6f6aea9a1ae8566cae9 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -349,9 +349,38 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "</select><br />";
msg += "<br /><input type=\"submit\" value=\"Store\"/></form>";
+ } else if ( perf.equals("prmtrimonet") ){
+
+ String sel = params.getProperty("id");
+ msg ="<h1>Trim networks</h1><form action=\"trimonet\">";
+ msg += "Network: <select name=\"id\">";
+ for ( OntologyNetwork on : manager.ontologyNetworks() ) {
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ if ( sel != null && sel.equals( id ) ){
+ msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
+ } else { msg += "<option value=\""+id+"\">"+pid+"</option>";}
+ }
+ msg += "</select><br />";
+ msg += "Type: <select name=\"type\"><option value=\"hard\">hard</option><option value=\"perc\">perc</option><option value=\"best\">best</option><option value=\"span\">span</option><option value=\"prop\">prop</option></select><br />Threshold: <input type=\"text\" name=\"threshold\" size=\"4\"/> <small>A value between 0. and 1. with 2 digits</small><br /><input type=\"submit\" name=\"action\" value=\"Trim\"/><br /></form>";
+
+ } else if ( perf.equals("trimonet") ){
+ Message answer = manager.trimonet( params );
+ if ( answer instanceof ErrorMsg ) {
+ System.out.println("answer error ");
+ msg = testErrorMessages( answer, params, eSource );
+ } else {
+ msg ="<h1>Trimed network</h1><form action=\"trimonet\">";
+ msg += "<a href=\"" + answer.getContent() +"\">" + answer.getContent() + "</a>";
+
+ System.out.println("answer: "+ answer.getContent());
+ }
+
} else if ( perf.equals("prmmatchonet") ){
msg = "<h1>Match an ontology network</h1><form action=\"matchonet\">";
+ msg += "<h2><font color=\"red\">(not implemented yet)</font></h2>";
msg += "Network: <select name=\"id\">";
String sel = params.getProperty("id");
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
@@ -385,7 +414,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("matchonet") ) {
- // DO MATCHING
+ // DO MATCHING version 1
+
List<Message> answer = manager.alignonet( params );
msg = "<h1>Network Alignments results</h1>";
Iterator<Message> it = answer.iterator();
@@ -396,11 +426,12 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
}
msg += "</ul>";
- /*
+
+
// DO MATCHING
- String idON = params.getProperty("id");
+/* String idON = params.getProperty("id");
logger.debug("Matching network {}", idON);
- Message answer = manager.alignonet( params );
+ Message answer = manager.alignonet2( params );
if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource );
} else {
@@ -420,7 +451,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
}
msg += "</ul>";
}
- */
+ */
} else if ( perf.equals("prmretreiveonet") ){
@@ -456,6 +487,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("prmcloseonet") ){
msg = "<h1>Close an ontology network</h1><form action=\"matchonet\">";
+ msg += "<h2><font color=\"red\">(not implemented yet)</font></h2>";
msg += "Network: <select name=\"id\">";
String sel = params.getProperty("id");
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
@@ -472,7 +504,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<input type=\"submit\" name=\"action\" value=\"Compose\"/> ";
msg += "<input type=\"checkbox\" name=\"new\" /> New ";
- } else if ( perf.equals("prmresetonet") ){
+ } else if ( perf.equals("prmnormalizeonet") ){
} else if ( perf.equals("") ) {
msg = "<h1>Ontology Network commands</h1>";
@@ -480,10 +512,11 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
// msg += "<form action=\"prmlistonet\"><button title=\"List networks stored in the server\" type=\"submit\">Available networks</button></form>";
msg += "<form action=\"prmloadonet\"><button title=\"Load a network from a valid source\" type=\"submit\">Load a network</button></form>";
msg += "<form action=\"prmstoreonet\"><button title=\"Store a network in the server\" type=\"submit\">Store network</button></form>";
+ msg += "<form action=\"prmtrimonet\"><button title=\"Trim a network\" type=\"submit\">Trim network</button></form>";
msg += "<form action=\"prmmatchonet\"><button title=\"Match an ontology network\" type=\"submit\">Match network </button></form>";
msg += "<form action=\"prmretreiveonet\"><button title=\"Render an ontology network in a particular format\" type=\"submit\">Render network</button></form>";
msg += "<form action=\"prmcloseonet\"><button title=\"Close an ontology network\" type=\"submit\">Close network</button></form>";
- msg += "<form action=\"prmresetonet\"><button title=\"Reset an ontology network\" type=\"submit\">Reset network</button></form>";
+ msg += "<form action=\"prmnormalizeonet\"><button title=\"Normalize an ontology network\" type=\"submit\">Reset network</button></form>";
msg += "<form action=\"../html/\"><button style=\"background-color: lightpink;\" title=\"Back to user menu\" type=\"submit\">User interface</button></form>";
} else {
msg = "Cannot understand: "+perf;
diff --git a/src/fr/inrialpes/exmo/align/service/SQLCache.java b/src/fr/inrialpes/exmo/align/service/SQLCache.java
index 39086e6a8cc850f2f38354b0bc3d1718ddba6f3b..4379a3839165f2b244db24da4255cd1965188de6 100644
--- a/src/fr/inrialpes/exmo/align/service/SQLCache.java
+++ b/src/fr/inrialpes/exmo/align/service/SQLCache.java
@@ -585,18 +585,21 @@ public class SQLCache extends VolatilCache implements Cache {
// Do not add transaction here: this is handled by caller
public void recordOntology( Statement st, URI uri, URI file, Ontology onto ) throws SQLException {
- String sfile = "";
+ // modify to use queryStatement.setNull for sformalism and sformuri
String suri = uri.toString();
+ String sfile = "";
if ( file != null ) sfile = file.toString();
+ String sformuri = "NULL";
String query = "SELECT * FROM ontology WHERE uri="+quote(suri)+";";
ResultSet res = st.executeQuery(query);
if ( !res.next() ) {
- logger.debug( "Recording ontology {} with file {}", suri, sfile );
+ logger.debug( "Recording ontology {} with file {} formalism {} formURI {}", suri, sfile, onto.getFormalism(), onto.getFormURI() );
if ( onto != null ) {
+ if ( onto.getFormURI() != null ) sformuri = onto.getFormURI().toString();
query = "INSERT INTO ontology " +
"(uri, file, formname, formuri) " +
- "VALUES ("+ quote(suri)+","+quote(sfile)+","+quote(onto.getFormalism())+","+quote(onto.getFormURI().toString())+")";
+ "VALUES ("+ quote(suri)+","+quote(sfile)+","+quote(onto.getFormalism())+","+quote(sformuri)+")";
} else {
query = "INSERT INTO ontology " +
"(uri, file) " +
@@ -604,9 +607,12 @@ public class SQLCache extends VolatilCache implements Cache {
}
st.executeUpdate(query);
} else {
+ String sformname = "";
+ if ( res.getString("formname") != null ) sformname = res.getString("formname");
if ( onto != null && res.getString("formname").equals("") ) { // JE: checktest
logger.debug( "Updating ontology {} with formalism {}", suri, onto.getFormalism() );
- query = "UPDATE ontology SET formname="+quote(onto.getFormalism())+", formuri="+quote(onto.getFormURI().toString())+" WHERE uri="+quote(suri)+";";
+ if ( onto.getFormURI() != null ) sformuri = onto.getFormURI().toString();
+ query = "UPDATE ontology SET formname="+quote(onto.getFormalism())+", formuri="+quote(sformuri)+" WHERE uri="+quote(suri)+";";
st.executeUpdate(query);
}
}
diff --git a/src/fr/inrialpes/exmo/align/service/VolatilCache.java b/src/fr/inrialpes/exmo/align/service/VolatilCache.java
index 89a88d053b8d6fd75df15a76492d21e20579d4f4..792005d6c63080b32e5e92e209b1fb56aaa69782 100644
--- a/src/fr/inrialpes/exmo/align/service/VolatilCache.java
+++ b/src/fr/inrialpes/exmo/align/service/VolatilCache.java
@@ -231,8 +231,7 @@ public class VolatilCache implements Cache {
private int randomNum() {
// We observe collisions!
- return Math.abs(rand.nextInt(1000));
- //return (int) (Math.abs(rand.nextInt(1000))+Math.random()*9);
+ return Math.abs(rand.nextInt(10000));
}
/*